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Crystal Structure of SB27 TCR in complex with HLA-B*3508-13mer peptide

X-ray diffraction
2.5Å resolution
PDB entry 2ak4 coloured by chain, front view.
PDB entry 2ak4 coloured by chain, side view.
PDB entry 2ak4 coloured by chain, top view.
Source organisms:
Assembly composition:
hetero pentamer (preferred)
Entry contents: 5 distinct polypeptide molecules

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Assemblies

Assembly 1
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Multimeric state: hetero pentamer
Accessible surface area: 37310.36 Å2
Buried surface area: 11967.14 Å2
Dissociation area: 1,276.67 Å2
Dissociation energy (ΔGdiss): 9.94 kcal/mol
Dissociation entropy (TΔSdiss): 12.22 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-134719
Assembly 2
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Multimeric state: hetero pentamer
Accessible surface area: 37772.42 Å2
Buried surface area: 12093.23 Å2
Dissociation area: 1,284.57 Å2
Dissociation energy (ΔGdiss): 9.46 kcal/mol
Dissociation entropy (TΔSdiss): 12.28 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-134719
Assembly 3 (preferred)
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Multimeric state: hetero pentamer
Accessible surface area: 37394.32 Å2
Buried surface area: 11626.32 Å2
Dissociation area: 1,007.49 Å2
Dissociation energy (ΔGdiss): -4.46 kcal/mol
Dissociation entropy (TΔSdiss): 13.83 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-134719
Assembly 4
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Multimeric state: hetero pentamer
Accessible surface area: 37143.54 Å2
Buried surface area: 11128.74 Å2
Dissociation area: 1,271.58 Å2
Dissociation energy (ΔGdiss): 8.69 kcal/mol
Dissociation entropy (TΔSdiss): 12.19 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-134719

Macromolecules

HLA class I histocompatibility antigen, B alpha chain
Chains: A, F, K, Q
Length: 276 amino acids
Theoretical weight: 31.98 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P01889 (Residues: 25-300; Coverage: 82%)
Gene names: HLA-B, HLAB
Pfam:
InterPro:
CATH:
SCOP:
HLA class I histocompatibility antigen, B alpha chain in PDB entry 2ak4, assembly 3, front view.
HLA class I histocompatibility antigen, B alpha chain in PDB entry 2ak4, assembly 3, side view.
HLA class I histocompatibility antigen, B alpha chain in PDB entry 2ak4, assembly 3, top view.
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Beta-2-microglobulin
Chains: B, G, L, R
Length: 99 amino acids
Theoretical weight: 11.75 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P61769 (Residues: 21-119; Coverage: 100%)
Gene names: B2M, CDABP0092, HDCMA22P
Pfam: Immunoglobulin C1-set domain
InterPro:
CATH: Immunoglobulins
SCOP: C1 set domains (antibody constant domain-like)
Beta-2-microglobulin in PDB entry 2ak4, assembly 3, front view.
Beta-2-microglobulin in PDB entry 2ak4, assembly 3, side view.
Beta-2-microglobulin in PDB entry 2ak4, assembly 3, top view.
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Lytic switch protein BZLF1
Chains: C, H, M, S
Length: 13 amino acids
Theoretical weight: 1.43 KDa
Source organism: Human herpesvirus 4 strain B95-8
Expression system: Not provided
UniProt:
  • Canonical: P03206 (Residues: 52-64; Coverage: 5%)
Gene name: BZLF1
Lytic switch protein BZLF1 in PDB entry 2ak4, assembly 3, front view.
Lytic switch protein BZLF1 in PDB entry 2ak4, assembly 3, side view.
Lytic switch protein BZLF1 in PDB entry 2ak4, assembly 3, top view.
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T cell receptor alpha chain constant
Chains: D, I, N, T
Length: 211 amino acids
Theoretical weight: 24.01 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P01848 (Residues: 1-93; Coverage: 66%)
Gene names: TCRA, TRAC
Pfam: Domain of unknown function (DUF1968)
InterPro:
CATH: Immunoglobulins
SCOP:
T cell receptor alpha chain constant in PDB entry 2ak4, assembly 3, front view.
T cell receptor alpha chain constant in PDB entry 2ak4, assembly 3, side view.
T cell receptor alpha chain constant in PDB entry 2ak4, assembly 3, top view.
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T cell receptor beta constant 1
Chains: E, J, P, U
Length: 245 amino acids
Theoretical weight: 27.64 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P01850 (Residues: 1-129; Coverage: 73%)
Gene name: TRBC1
Pfam: Immunoglobulin C1-set domain
InterPro:
CATH: Immunoglobulins
SCOP:
T cell receptor beta constant 1 in PDB entry 2ak4, assembly 3, front view.
T cell receptor beta constant 1 in PDB entry 2ak4, assembly 3, side view.
T cell receptor beta constant 1 in PDB entry 2ak4, assembly 3, top view.
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